Semantics for Biodiversity (S4BioDiv 2013) Proceedings of the First International Workshop on Semantics for Biodiversity May 27th 2013 Montpellier, France Pierre Larmande, Elizabeth Arnaud, Isabelle Mougenot, Clement Jonquet, Thérèse Libourel, Manuel Ruiz (editors) May 2013 Photo credit @ I. Mougenot Logo credit @ P. Larmande 2 Semantics for Biodiversity (S4BioDiv 2013) Proceedings of the First International Workshop on Semantics for Biodiversity Montpellier, France, May 27, 2013 In conjunction with ESWC 2013 (http://2013.eswc-conferences.org) Edited by Pierre Larmande * Elizabeth Arnaud ** Isabelle Mougenot *** Clement Jonquet **** Therese Libourel *** Manuel Ruiz ***** * IRD - UMR DIADE, France ** Bioversity International, Montpellier, France *** Université Montpellier 2 - UMR Espace-Dev, France **** Université Montpellier 2 - LIRMM, France ***** CIRAD - UMR AGAP, France Web site http://semantic-biodiversity.mpl.ird.fr On line proceedings CEUR Workshop Proceedings, volume 979 http://ceur-ws.org/Vol-979 3 Organization Committee Pierre Larmande (IRD - UMR DIADE, France), Organization Chair Isabelle Mougenot (UMII - UMR Espace DEV, France) co-Chair Thérèse Libourel (UMII - UMR Espace DEV, France) Clément Jonquet (UMII - LIRMM, France) Scientific Program Committee Elizabeth Arnaud (Biodiversity International), PC Chair Manuel Ruiz (CIRAD - UMR AGAP, France) Pierre Bonnet (CIRAD - UMR AMAP, France) Richard Bruskiewich (Bioversity International) Pascal Neveu (INRA - UMR MISTEA, France) Joel Sachs (University of Maryland, Baltimore County,USA) Julie Chabalier (Natural Solutions, France) Cyril Pommier (INRA - URGI - France) Mark Wilkinson (Polytechnic University of Madrid, Spain and University of British Columbia) Konstantin Todorov (UMII - UMR LIRMM, France) Pankaj Jaiswal (Oregon State University,USA) Xavier Sirault (CSIRO, Autralia) Caterina Caracciolo (FAO , Italy ) Lieke Verhelst (Wageningen University, The Netherlands) Damian Gessler (iPlant Collaborative, USA) Nikos Manouselis (Agro-Know, University of Alcala, Spain) Eamonn O Tuama (GBIF, University of Copenhagen , Denmark) Norman Morrison (NEBC, The University of Manchester, UK) 4 Foreword Semantic web standards, tools, ontologies and related technologies have considerably matured in the recent years. Nowadays, accessing a wide catalogue of biological, social, environmental, and ecological data sources helps stakeholders working on biodiversity to answer their complex questions. Will the real time access to web resources effectively support the definition of strategies to conserve and manage biodiversity? How might semantic web technologies help us to handle the complex and heterogeneous big data related to biodiversity? The workshop aims to identify the key challenges faced by the bioinformatics community, discuss potential solutions and identify the opportunities emerging from the trans- disciplinary interactions between Plant Science and Informatics experts. Therefore, we expect the bioinformatics experts to explain how they apply semantic web standards and tools to their scientific topic, from biology, agriculture, agro-ecology, genomics, environmental studies, to social sciences, citizen sciences. Research papers presenting various aspects of semantic web technologies applied to biodiversity data, ranging from position papers to implemented systems descriptions and their evaluation have been selected. We have received 15 papers and selected 11 of them for the workshop, including 5 papers with long presentations and 6 papers with short presentations during the workshop. In addition, the workshop has offered two keynote presentations that are also mentioned hereafter. We thanks the organization of the 10th ESWC 2013 for hosting the S4BioDiv workshop as a joint event and the Polytech’Montpellier engineering school for rooms and local arrangements in the beautiful city of Montpellier. Finally, we like to acknowledge our sponsors for the event, listed in the last page of the proceedings and thanks the scientific program committee for the reviewing of papers and discussion during the workshop presentations and panels. The editors 5 Keynotes Mark Wilkinson (Centro de Biotecnología y Genómica de Plantas UPM-INIA) Web Science: A Distributed, Explicit, Transparent, Automated, Reusable, and Reproducible Experiments Projections suggest that the delay between scientific discovery, and the dissemination and implementation of the knowledge embodied in that discovery, will soon vanish. At that point, all knowledge resulting from an investigation will be instantly interpreted and disseminated, influencing other researcher's experiments, and their results, immediately and transparently. This clearly requires that research results be of extremely high quality and reliability, and that research processes – from hypothesis to publication – become tightly integrated into the Web. Though the technologies necessary to achieve this kind of “Web Science” do not yet exist, our recently-published studies of automated in silico investigation demonstrate that we are enticingly close, and a path toward next-generation Web Science is now clear. The Web, to date, has only cosmetically changed the research process. Semantic Web Science, however, re-defines scientific methodology by fully integrating it with a global network of knowledge and expertise on the Semantic Web. Olivier Rovellotti (Natural Solutions) Semantic for Biodiversity: a user’s perspective In order to provide enlightened governance of our biodiversity heritage; it is crucial to gather and analyze as much biodiversity observational data as possible. Data gathering programs can be plotted on a scale of complexity and scope, from citizen science to professional environmental assessments. The data collected is so heterogeneous in quality, granularity and precision that it requires advanced data management techniques. Using semantic web technologies allows us to give various agents the correct tool to assist them in the entire process. Throughout our daily work in improving the data gathering, data aggregation and data visualization, we are able to give feedback on ours attempts at integrating semantic web technology in practical solutions. 6 Workshop articles A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data Rathachai Chawuthai, Hideaki Takeda, Vilas Wuwongse, Utsugi Jinbo p. 09-16 Publishing and Using Plant Names as an Ontology Service Jouni Tuominen, Nina Laurenne, Eero Hyvonen p. 17-24 A Faceted Search System for Facilitating Discovery-driven Scientific Activities: A Use Case from Functional Ecology Marie-Angélique Laporte, Eric Garnier, Isabelle Mougenot p. 25-36 Crop Ontology: Vocabulary for Crop-related Concepts Matteis Luca, Pierre-Yves Chibon, Herlin Espinosa, Milko Skofic, Richard Finkers, Richard Bruskiewich, Glenn Hyman, Elizabeth Arnaud p. 37-45 A Case-Study of Ontology-Driven Semantic Mediation of Flower-Visiting Data from Heterogeneous Data-Stores in Three South African Natural History Collections Willem Coetzer, Deshendran Moodley, Aurona Gerber p. 47-61 Flexible Scientific Data Management for Plant Phenomics Research Peter Ansell, Robert Furbank, Kutila Gunasekera, Jianming Guo, David Benn, Gareth Williams, Xavier Sirault p. 63-70 Lightweight Ontology-Based Tools for Managing Observational Data Shawn Bowers, Riley Englin, Carlos Fonseca, Paul Jewell, Lauren Joplin, Patrick Mosca, Tyler Pacheco, Jacob Troxel, Tyler Weeks p. 71-86 BirdWatch--Supporting Citizen Scientists for Better Linked Data Quality for Biodiversity Management Eero Hyvonen, Miika Alonen, Mikko Koho, Jouni Tuominen p. 87-99 iPlant SSWAP (Simple Semantic Web Architecture and Protocol) Enables Semantic Pipelines for Biodiversity Damian Gessler, Blazej Bulka, Evren Sirin, Hans Vasquez-Gross, John Yu, Jill Wegrzynp. 101-110 A Knowledge Base for Exploited Marine Ecosystems Barde Julien, Pascal Cauquil, Billet Norbert p. 111-120 Detecting Semantic Overlap and Discovering Precedents in the Biodiversity Research Literature Graeme Hirst, Nadia Talent, Sara Scharf p. 121-131 7 ^ĞŵĂŶƚŝĐƐĨŽƌŝŽĚŝǀĞƌƐŝƚLJtŽƌŬƐŚŽƉ;^ϰŝŽŝǀϮϬϭϯͿ͕DŽŶƚƉĞůůŝĞƌ͕&ƌĂŶĐĞ A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data Rathachai Chawuthai1, Hideaki Takeda2, Vilas Wuwongse3, and Utsugi Jinbo4 1 Asian Institute of Technology, Prathumtani, Thailand 2"4)"$)"*$(."*-$0. 2 National Institute of Informatics, Tokyo, Japan 4",&%"/**"$+1 3 Thammasat University, Prathumtani, Thailand 76*-"3&/(245"$4) 4 National Museum of Nature and Science, Tokyo, Japan 5+*/#0,")",5(0+1 Abstract. The variety of classification systems and the new discovery of taxonomists lead to the diversity of biological information, especially taxon concepts. The association among taxon concepts across research institutes is very difficult to establish, because there is no single interpretation of the name of a taxon concept. Owing to this difficulty, further integration of more biological knowledge is very complicated when they deal with many sources of data or depending on different taxon concepts. This research aimes to develop a framework for linking some multiple related taxon concepts across research repositories, and preserving background knowledge of their changes. Therefore, we propose a logical model for taxon concepts in Resource Description Framework (RDF). Herewith, we implement a prototype to demonstrate the feasibility of our approach. It has been found that our model can publish taxon information as linked data and, hence, with additional benefits